Re: [Freesurfer] Making a surface from the skull?
Thanks for these suggestions - looks promising so far! mjp On Oct 1, 2010, at 4:32 PM, Nick Schmansky wrote: > also, once you get a surface file, then mris_convert will convert > to .stl format, which we've used in 3d printer applications. > > if you can get a skull from mri_watershed, then mri_tessellate will make > a surface. mris_smooth and mris_keep_main_component are two other useful > utility to clean things up. > > n. > > On Fri, 2010-10-01 at 16:24 -0400, Bruce Fischl wrote: >> Hi Mark, >> >> you might check Matti Hamalainen's MNE website. He uses the watershed code >> to generate boundary models, including skull. Or just try out mri_watershed >> with -surf I think (it's covered in the help, at least a bit) >> >> cheers >> Bruce >> >> >> On Fri, 1 Oct 2010, Mark J. Pearrow wrote: >> >>> Hi all, >>> >>> I know this is slightly outside the normal bounds, but I am wondering if >>> there is a way to create a surface from the skull? One of our folks is >>> looking to create some custom-fitted recording chambers for nonhuman >>> primates based on the individual skull. I seem to recall that FS has a way >>> of generating STL files, which would be perfect for submitting to a rapid >>> prototyping machine. Here's what the user says: >>> >>> " In brief, I would like to shape the bottom-side of my recording chambers >>> (elliptical/circular cylinder) so that they form-fit to the curvature of >>> the primate skull. Ideally, this will involve segmenting and extracting a >>> 3D portion of the skull and converting it into an STL file to use for >>> machining the implant." >>> >>> Best, >>> >>> mjp >>> >>> >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Making a surface from the skull?
Hi all, I know this is slightly outside the normal bounds, but I am wondering if there is a way to create a surface from the skull? One of our folks is looking to create some custom-fitted recording chambers for nonhuman primates based on the individual skull. I seem to recall that FS has a way of generating STL files, which would be perfect for submitting to a rapid prototyping machine. Here's what the user says: " In brief, I would like to shape the bottom-side of my recording chambers (elliptical/circular cylinder) so that they form-fit to the curvature of the primate skull. Ideally, this will involve segmenting and extracting a 3D portion of the skull and converting it into an STL file to use for machining the implant." Best, mjp ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] segfault from freeview.bin
Hi all, We are consistently getting segfaults with core dumped from freeview.bin when trying to open MGZ files that are larger than some (undetermined) threshold. We are running the 4.5.0 CentOS 4 x86_64 binary package on Ubuntu 9.04 Workstation. Upon opening freeview and attempting to load one of the larger files, the application crashes and dumps core, and leaves the following in the error.log: CTABreadASCII(/u2/meeshy/Desktop/Amy Activation Screenshots/SAD_022/lh_Novelobjects_social/EFvNF.png): badly formed file mghRead: encountered error executing: 'zcat /u2/meeshy/Desktop/I29/flash20_100um_avg_rotatedKH2009_mfg_new.mgz',frame -1, errno 12 mghRead: encountered error executing: 'zcat /u2/meeshy/Desktop/I29/flash20_100um_avg_rotatedKH2009_mfg_new.mgz',frame -1, errno 12 (running that same zcat command from the command line works fine) Loading the resulting core into gdb: mee...@ba7:~$ gdb `which freeview.bin` ./core [mumble mumble reading symbols] ... Core was generated by `freeview.bin'. Program terminated with signal 11, Segmentation fault. [New process 2415] #0 0x7f1c91defcd0 in ?? () from /usr/lib/libGL.so.1 (gdb) list 1 /usr/pubsw/packages/vtk/5.2.0/src/Utilities/DICOMParser/DICOMFile.cxx: No such file or directory. in /usr/pubsw/packages/vtk/5.2.0/src/Utilities/DICOMParser/DICOMFile.cxx (gdb) bt #0 0x7f1c91defcd0 in ?? () from /usr/lib/libGL.so.1 #1 0x7f1c91de430f in _fini () from /usr/lib/libGL.so.1 #2 0x7f1c9257f354 in ?? () from /lib64/ld-linux-x86-64.so.2 #3 0x7f1c89f2d6ed in exit () from /lib/libc.so.6 #4 0x7f1c89f155ad in __libc_start_main () from /lib/libc.so.6 #5 0x005b89ea in _start () These are around 250MB in size. Smaller files load just fine. mjp ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] qdec error
It's possible that you are running a Debian-based distro and just don't have libtiff.so.3; but you probably have libtiff.so.4, so you can create a symlink so that libtiff.so.3 points to libtiff.so.4. I have to do this In Debian "etch" and later mjp On Nov 26, 2008, at 4:26 PM, "Siddharth Srivastava" <[EMAIL PROTECTED]> wrote: Hi Prapti, I think you have to modify the $LD_LIBRARY_PATH shell variable. first find where libtiff.so.3 is. Usually "locate libtiff.so.3" will tell you where the file is at. On my machine, it is in /usr/lib/ and /usr/ lib64/ then LD_LIBRARY_PATH = $LD_LIBRARY_PATH:/usr/lib64/ export LD_LIBRARY_PATH qdec This should work. On Wed, Nov 26, 2008 at 12:19 PM, Prapti Gautam <[EMAIL PROTECTED] > wrote: Hi, I've run across the following error while trying to run qdec in my linux 64 bit computer, qdec.bin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory Is there any specific file that I need to download or change configuration of? I apologise if this has been covered before in the mailing list, Any help is greatly appreciated, Thanks, Prapti ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer display problems
hi Sid, This should be done on the server side - where you are processing the data. For example, I have a Dell PowerEdge 1950 that is running 64-bit Debian Gnu/Linux and has Freesurfer/fsfast installed. I log into it from my Mac, which is running os x. So I needed to add those libraries to the Dell machine to make things work. My systems are 64 bit, so I think the instructions I gave should work for you, too. mjp On Nov 19, 2008, at 1:21 PM, Siddharth Srivastava wrote: Hi mjp, Thanks for an account of a working solution to the problem. I just wanted to know if this intervention has to done on the client machine (from where i am viewing the results), or on the server side (on which i am processing the data)? Further, in case of a 64 bit machine, would the source and the destination directories change accordingly? best regards, sid. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer display problems
Hi all, This is a bug that has baffled me for almost a year now, so today I decided to just attend to it exclusively. I have never understood why, exactly, the anecdotal and illogical fix for the sliver-of-the-brain issue seems to be to install an NVidia graphics card in the afflicted server. I found this posting: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2008-April/007558.html Which seemed to indicate that it was not the card itself that made the difference, but rather some software component that made things work. There is an extension to X11, called GLX, which allows the remote side (the "client", in X11 speak) to bypass the processing of OpenGL commands and to send them to the server. So, following the advice in the posting above, I downloaded the latest NVidia.run package and unpacked it by using the "-x" flag - then I copied all of the usr/lib/ and usr/lib32/ difrectories in the (freshly unpacked) NVIDIA-linux directory into /usr/lib and /usr/lib32, respectively. Then I ran "ldconfig -v" to update the ld cache. And voila, I can run tksurfer over X11, VNC and NX now on a server that has no NVidia card, without any problems. I still don't understand what exactly is being provided by NVidia's version of the libraries, but I suspect it has to do with "TLS" (in the context of OpenGL, not in the crypto sense). This appeared in the output of `ldd tksurfer.bin` on my systems with nvidia cards, and on my previously-broken system after I installed those files: libnvidia-tls.so.1 => /usr/lib/tls/libnvidia-tls.so.1 mjp On Nov 18, 2008, at 9:35 PM, Bruce Fischl wrote: Hi Sid, this is a known problem. It actually used to work and we broke it. The current workaround is to use VNC. cheers, Bruce On Tue, 18 Nov 2008, Siddharth Srivastava wrote: Hi ! I am a relatively new user of freesurfer, and currently i have 2 instances of the same -stable 64bit Linux versions installed, one on my local machine, and the other on a cluster, accessible over the network. I have been able to get freesurfer running without any problems on my local machine, but after i installed the same version on the remote machine, the tksurfer window did not display what i expectd to see, but only a small part of the data (%tksurfer bert lh inflated). This small patch responds to all commands from the GIU, but that is all that i see. I have trawled through the archives, both old and new, and there have been references to similar problems, without any definitive way to solve it. What exact aspect of the system configuration has to be examined/re-worked to solve it? Does anyone have any experience with this kind of problem? with regards, sid. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] qdec.table.dat error
Check out this article: https://wiki.ubuntu.com/DashAsBinSh /bin/sh is still just a symlink to /bin/bash on Debian. mjp On Oct 8, 2008, at 2:43 PM, Mishkin Derakhshan wrote: Hi Nick, I tried unalias -a and then runnig qdec but it didn't work either. I think the problem is with bash vs. sh in ubuntu (possible all debian systems). ie. /bin/sh is not the same as /bin/bash so not all bash commands will work. I did this: sudo mv /bin/sh /bin/sh.bak sudo ln -s /bin/bash /bin/sh and then it worked. I'm hoping this doesn't have repercussion for my other programs though. thanks, mishkin On Tue, Oct 7, 2008 at 11:20 PM, Nick Schmansky <[EMAIL PROTECTED]> wrote: yes, this sounds like a tough one. the VerifySubjects routine that produces that error message just runs the 'ls' command on that subject directory name, so that is why i asked. if you run the 'ls' command on '/lab1/FreeSurfer/4.0.5/ms-mni/testing/tester', does it return a correct response? ie a non-zero status? what does 'which ls' say? possibly it is aliased to something that is causing a problem. does qdec work despite the error? the code is setup to just print the error, but continue anyway. if the subject doesnt exist, it will fail downstream (during mri_glmfit). i'll try to think of other things. nick On Tue, 2008-10-07 at 21:26 -0400, Mishkin Derakhshan wrote: Hi Nick, Yes I've checked most of the obvious things I could think of. The directories all exist, permissions on all files are 775, i will try 777 but don't suspect that will make a difference. My env variables seem to be set properly as well. opus[/lab1/FreeSurfer/4.0.5/ms-mni/testing/tester]$ . /lab1/FreeSurfer/4.0.5/quarantine/SetUpFreeSurfer.sh freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /lab1/FreeSurfer/4.0.5/quarantine FSFAST_HOME /lab1/FreeSurfer/4.0.5/quarantine/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /lab1/FreeSurfer/4.0.5/ms-mni/testing/ MNI_DIR /lab1/FreeSurfer/4.0.5/quarantine/mni I get the same error when trying to load the tutorial qdec.table.dat as well. My analysis is stuck at this point so any help is greatly appreciated. thanks, mishkin On Tue, Oct 7, 2008 at 7:27 PM, Nick Schmansky <[EMAIL PROTECTED]> wrote: Mishkin, Does this directory exist? /lab1/FreeSurfer/4.0.5/ms-mni/testing/tester The error message you are seeing is checking for the existence of that directory. Nick On Tue, 2008-10-07 at 14:30 -0400, Mishkin Derakhshan wrote: Hi, When I try to load a qdec.table.dat I always get the same error: sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'tester' in SUBJECTS_DIR I've tried digging around through the archives and still can't seem to find a solution for this problem. I've tried tcsh and the bash shell. Here is a bit more information and my qdec.table.dat is attached. Any ideas on how to get qdec up and running would be very useful. thanks, mishkin FREESURFER_HOME: /lab1/FreeSurfer/4.0.5/quarantine Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5 Debian version: lenny/sid Kernel info: Linux 2.6.24-18-generic x86_64 opus:/lab1/FreeSurfer/4.0.5/ms-mni/testing> qdec & opus:/lab1/FreeSurfer/4.0.5/ms-mni/testing> Reading /lab1/FreeSurfer/4.0.5/quarantine/lib/tcl/tkUtils.tcl Using /lab1/FreeSurfer/4.0.5/quarantine/lib/tcl/fsgdfPlot.tcl Loading data table /lab1/FreeSurfer/4.0.5/ms-mni/testing/qdec/ qdec.table.dat... Setting SUBJECTS_DIR to '/lab1/FreeSurfer/4.0.5/ms-mni/testing' Number of columns: 4 fsid column:1 Number of factors: 3 Number of subjects: 2 Reading discrete factor levels from config file /lab1/FreeSurfer/4.0.5/ms-mni/testing/qdec/ gender.levels...'Male','Female', done. Data table /lab1/FreeSurfer/4.0.5/ms-mni/testing/qdec/ qdec.table.dat loaded. SUBJECTS_DIR is '/lab1/FreeSurfer/4.0.5/ms-mni/testing' sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'tester' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'tester2' in SUBJECTS_DIR Error loading the data table. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer woes
Hi all, FYI, this same problem has been bugging me for several months. Most ATI chipsets have a nice driver installer bundle that, once installed, will let you run tksurfer without a problem. However, this particular chipset, the ES1000, which is the chipset on Dell PowerEdge servers, is unsupported and seems to have been abandoned by ATI/AMD/whoever they are this week. If you happen to be unlucky enough to have Dell PowerEdge servers with this chipset and the need to run tksurfer, you're out of luck, until you put a slightly "better" graphics card in. I just managed to install an nVidia 8400GS (the x1 PCI-e version - the poweredge PCI-e bus is x8, which means it won't work with any of the most recent cards, but will work with slightly older x1 cards) and tksurfer works fine now. I can provide the gory details if you're in this boat. mjp On Sep 8, 2008, at 9:14 AM, Hoptman, Matthew wrote: Hi all, I’m having trouble using freesurfer’s tksurfer program (I only get a sliver of the brain). Here is the error info I get: [ghidra: subjects]$ tksurfer 77059 lh pial surfer: current subjects dir: /home/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/freesurfer/subjects surfer: Reading header info from /home/freesurfer/subjects/77059/mri/ T1.mgz surfer: vertices=184362, faces=368720 Loading /home/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(77059) surfer: using interface /home/freesurfer/lib/tcl/tksurfer.tcl Reading /home/freesurfer/lib/tcl/tkm_common.tcl Reading /home/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... The driver info (from /etc/X11/xorg.conf) is: Section "Device" BoardName"ES1000 515E" BusID"14:13:0" Driver "radeon" Identifier "Device[0]" Option "GARTSize" "32" Option "usevnc" "yes" Section "DRI" Group "video" Mode 0660 EndSection I’m have an onboard ATI ES1000 515E graphics chip. Any ideas?? Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e- mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Segfault in mris_fwhm?
Hi all, I've run into a snag whilst running mris_fwhm: $ mris_fwhm --i /all.nii --s --hemi rh --sum / fwhm.sum rh white Number of vertices 136129 Number of faces272254 Total area 88745.070312 GroupSurface 0 FIX_VERTEX_AREA 1 AvgVtxArea 0.651919 AvgVtxDist 0.883205 StdVtxDist 0.255280 Polynomial detrending, order = 0 Computing spatial AR1 ERROR: MRISar1: Surf/Src dimension mismatch. Segmentation fault All of the unpacking, reconstruction, and preprocessing up till that point have all been done using a pretty typical FS stream (with the exception of not smoothing in the volume) using FS 4.0.5. The segfault happens with both the mris_fwhm binary that comes with FS 4.0.5 and with the one I built from last night's CVS tree. I haven't run it under a debugger yet but was wondering if this has been seen before, etc. mjp ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer woes
Hi Matthew, This is the typical symptom of either not having the right OpenGL libraries and/or not having a driver that supports the 3d stuff. That particular chip (ES1000) seems to be an orphan as far as Linux support goes - I haven't found a driver installation package on the ATI/AMD site that purports to support it. I'd be interested in hearing which linux distro you are using and which flavor radeon driver you're using. Is this a Dell PowerEdge server? I have a bunch of them that I can't run tksurfer on for the same reason. So far I've been using a workstation that has an Nvidia card, which works properly with the NVidia proprietary driver installed. mjp On Sep 8, 2008, at 9:14 AM, Hoptman, Matthew wrote: Hi all, I’m having trouble using freesurfer’s tksurfer program (I only get a sliver of the brain). Here is the error info I get: [ghidra: subjects]$ tksurfer 77059 lh pial surfer: current subjects dir: /home/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/freesurfer/subjects surfer: Reading header info from /home/freesurfer/subjects/77059/mri/ T1.mgz surfer: vertices=184362, faces=368720 Loading /home/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(77059) surfer: using interface /home/freesurfer/lib/tcl/tksurfer.tcl Reading /home/freesurfer/lib/tcl/tkm_common.tcl Reading /home/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... The driver info (from /etc/X11/xorg.conf) is: Section "Device" BoardName"ES1000 515E" BusID"14:13:0" Driver "radeon" Identifier "Device[0]" Option "GARTSize" "32" Option "usevnc" "yes" Section "DRI" Group "video" Mode 0660 EndSection I’m have an onboard ATI ES1000 515E graphics chip. Any ideas?? Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e- mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] error while loading shared libraries:libtiff.so.3
libtiff.so.3 is typically provided by the ia32-libs package in Ubuntu and Debian (and presumably any other Debian-derived distros) So you can install using the following command: sudo aptitude install ia32-libs I'm not sure which binary is doing the complaining, I don't see anything in $FREESURFER_HOME/bin that is linked against libtiff3 but I remember having to install the 32-bit compat library to make stuff work. HTH, mjp On Aug 13, 2008, at 3:35 PM, lan lin wrote: I'm using 64 bit Ubuntu and installed freesurfer-Linux-rh9-stable- pub-v4.0.5-full.tar.gz Everything worked fine when I tested the installation with tkmedit and tksurfer. I then ran recon-all and got error message while loading shared libraries:libtiff.so.3. I have tried ln /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3 But still got same error message. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] libXmu error on cluster
Hi Pedro, What do you see if you run the following command: ldd /usr/lib/libXmu.so.6 Once you fix the problem, if you are running FreeSurfer 4, I *think* you can re-run recon-all with the -make flag and it will just do the processing that got missed. mjp On Mar 22, 2008, at 9:51 PM, Pedro Paulo Oliveira Jr wrote: Hi, I ran 40 process and all finished with /b/03/netfi01/freesurfer/subjects/rodiguespierinam/scripts/recon- all.log:mris_volmask.bin: error while loading shared libraries: libXmu.so.6: cannot open shared object file: No such file or directory But in /usr/lib there is a libXmu.so.6 My questions are: 1) Anybody know why it failed? 2) If I fix this how can I run recon-all from this point? Thanks PPJ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] CentOS 5.1 and freesurfer and tksurfer
Hi Dhruman, I had this problem with a Debian (Etch) system with an ATI card, and the way I got it to work was to install the fglrx driver for the ATI card. I also was missing a bunch of OpenGL stuff, too, but I think the driver was the main issue. I'm unfamiliar with CentOS but these instructions seem to make sense: http://www.linlap.com/wiki/Configuring+the+fglrx+driver+for+ATI+graphics+chips+in+CentOS+and+RHEL+5 mjp On Mar 6, 2008, at 10:15 AM, Goradia, Dhruman D wrote: Hi all, I am facing the same problem with CentOS 5 and tksurfer.Is there any fix for this problem? Thank you, -Dhruman -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Nick Schmansky Sent: Tuesday, February 19, 2008 10:03 AM To: [EMAIL PROTECTED] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] CentOS 5.1 and freesurfer and tksurfer Does glxgears work? That is an app that comes with Linux that exercises the GLX (OpenGL X extension) code. On Tue, 2008-02-19 at 20:41 +0800, [EMAIL PROTECTED] wrote: Dear FS experts, I install CentOS 5.1 and latest version of ATI driver and FS4.0.2, when I start tkmedit, it looks fine. In tksurfer, it just appear a sliver of surface without error message. In console, it stock on reading vertex. Is there anyway to correct it ? Thanks replay Kl chen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
